Here is how my batt banks are set up:
2 Group 31 batts for the house. They are on a 1, 2, both, off. 99.9% of the time it is on both. The only reason I have the switch installed is because I already had it. It is nice to be able to disconnect the batts when working on the electrical without having to remove the leads from the batt posts.
1 Group 24 start batt. This runs everything I need for the Atomic 4 engine. i.e. the blower, starter, spark plugs, fuel pump, etc. This is controlled with a 4 pos ignition switch. I highly recommend getting the 4 pos switch. Life is much easier now that I installed it.
The house and start banks are connected through an ACR. I am able to bypass this with a combiner switch. I am also able to turn off the auto combining via a breaker on my elec panel. This came in handy when my house bank would not hold a charge, but my start bank was fine.
I run all charging sources (except shore charger) to my house bank. Since it has more capacity than the start bank when the two are combined it will not draw down the house bank too much to equalize the two.
I find this system to be very simple, redundant, and relatively affordable.